8C3T | pdb_00008c3t

Structure of the GIsul2 transposon excisionase

PDB DOI: https://doi.org/10.2210/pdb8C3T/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Achromobacter xylosoxidans NBRC 15126 = ATCC 27061
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-12-28 Released: 2024-01-10
Deposition Author(s): Smyshlyaev, G., Arinkin, V., Barabas, O.
Funding Organization(s): European Commission, German Federal Ministry for Education and Research, EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.214 (Depositor), 0.212 (DCC)
R-Value Work:
0.199 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8C3T

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structures of transposon end complexes explain antibiotic resistance transfer across diverse bacteria

Smyshlyaev, G., Isbilir, B., Arinkin, V., Rojas-Cordova, C., Bateman, A., Barabas, O.

To be published.

Macromolecule Content

Total Structure Weight: 8.52 kDa
Atom Count: 503
Modeled Residue Count: 57
Deposited Residue Count: 73
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AlpA family phage regulatory protein	A	73	Achromobacter xylosoxidans NBRC 15126 = ATCC 27061	Mutation(s): 0 Gene Names: I6G72_19430
UniProt
Find proteins for A0AAN0NNU2 (Achromobacter xylosoxidans NBRC 15126 = ATCC 27061) Explore A0AAN0NNU2 Go to UniProtKB: A0AAN0NNU2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAN0NNU2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.214 (Depositor), 0.212 (DCC)
R-Value Work: 0.199 (Depositor), 0.200 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.305	α = 90
b = 39.305	β = 90
c = 71.582	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-01-10

Deposition Author(s):

Funding Organization	Location	Grant Number
European Commission	European Union	866250
German Federal Ministry for Education and Research	Germany	01KI1706
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND	Germany	291772

Revision History (Full details and data files)

Version 1.0: 2024-01-10
Type: Initial release
Version 1.1: 2024-11-13
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.